User: andres.firrincieli

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Posts by andres.firrincieli

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Subset WGCNA results for export to Cytoscape
... I wasn't able to replicate your error, but I might have an alternitive solution: module = "green" datexpr_green = datExpr[moduleColors == module,moduleColors == module] TOM_green = TOMsimilarityFromExpr(datexpr_green, power = 18, networkType = "signed", TOMType="signed"); probes = n ...
written 15 days ago by andres.firrincieli20
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Comment: C: Extracting VST matrix with batch effects removed
... Hi, have a look at this post: [https://support.bioconductor.org/p/62954/][1] [1]: https://support.bioconductor.org/p/62954/ ...
written 16 days ago by andres.firrincieli20
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Comment: C: Subset WGCNA results for export to Cytoscape
... Hi Charles, I have encountered this problem before. Can you give me the the results of `dim(datExpr)` and `dim(TOM)`? ...
written 16 days ago by andres.firrincieli20
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Comment: C: WGCNA: 1) low soft thresholding power, 2) large modules, 3) best correlation for
... > 1) According to the tutorial recommendations I would need to choose a > soft thresholding power of 3, since it reaches already R^2 of 0.8 and > is also the maximum. However, the power recommendations in the table > of the FAQs suggest a power of 6-12 for my sample size. What would you ...
written 28 days ago by andres.firrincieli20
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Comment: C: WGCNA: correlations module-traits, and module membership-gene significance
... For trait 6 I do not see anything wrong. None of the hub genes (genes with the highest module membership) in the turquoise module show a strong correlation with the trait 6. Also, the majority of the genes in the turquoise module show a correlation (pearson) < 0.1 with that trait: geneTrai ...
written 4 weeks ago by andres.firrincieli20
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Comment: C: how to filter genes in significant module?
... Hi Modarzi, You could run a Gene Enrichment Analysis on modules without filtering, and then focus on the hub of the module i.e., the genes with the highest [intramodular connectivity][1]. The hub could includes genes that are known to be involved in that specific pathway. [1]: https://www.rdocum ...
written 3 months ago by andres.firrincieli20
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cluserRepro for IGP calculation - long running time
... Dear All, I am using the clusterRepro function to calculate the In-Group Proportion (IGP) of a network of 13000 genes. I have launched the analysis 9 days ago and it is still ongoing. I am aware that clusterRepro can take days, even weeks, for the IGP calculation so my question is: how long would i ...
clusterrepro written 2.5 years ago by andres.firrincieli20

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